MolNFT v1 · #72966 · protein
Crystal structure of a pfam DUF849 domain containing protein (REUT_A1631) from ralstonia eutropha JMP134 at 1.90 a resolution
3NO5 · Uncharacterized protein: “Crystal structure of a pfam DUF849 domain containing protein (REUT_A1631) from ralstonia eutropha JMP134 at…”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.73). MolNFT v1 #72966 on…
- PDB
- 3NO5
- Type
- protein
- Length
- 1,638 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q471D6
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Uncharacterized protein | protein | 273 | 40% helix, 19% strand | Q471D6 |
| B, D | Uncharacterized protein | protein | 272 | 39% helix, 19% strand | Q471D6 |
| E | Uncharacterized protein | protein | 275 | 40% helix, 19% strand | Q471D6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.73 | 0.78 | 91 | EDO |
| 2 | 648 | 0.73 | 0.80 | 77 | ZN, EDO, ACT |
| 3 | 338 | 0.70 | 0.83 | 46 | empty |
| 4 | 360 | 0.70 | 0.83 | 48 | ZN |
| 5 | 324 | 0.70 | 0.83 | 44 | ZN |
Interfaces
6 interfaces between chains.
- E–F · 1171 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1170 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1156 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 533 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 527 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 61 modified (engineered).
Compared structures
- 3NO5 · Crystal structure of a Pfam DUF849 domain containing protein (Reut_A1631) from Ralstonia… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q471D6
- Elsewhere: RCSB PDB 3NO5 · PDBe 3NO5 · UniProt Q471D6
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